Initial release of pycytominer

Pycytominer release v0.1

Pycytominer is a python package that implements functions for every step of the image-based profiling pipeline.

Processing image-based readouts of cell morphology, we can now:

• aggregate single cells to form bulk profiles
• subsample single cells to form pseudo bulk replicates
• normalize both single cells and bulk profiles
• apply feature selection functions to remove uninformative morphology features
• generate consensus signatures from replicates

The package currently has 98% test coverage and is fully documented with some examples. We hope that you enjoy using pycytominer, and please report bugs, make recommendations, and discuss any ideas you might have.

What's Changed

• Adding Initial Functions by @gwaygenomics in #1
• Update LICENSE file by @gwaygenomics in #2
• Adding Travis yml by @gwaygenomics in #3
• Add normalize function by @gwaygenomics in #4
• Adding setup.py by @gwaygenomics in #7
• Add Cytominer Authors to Setup by @gwaygenomics in #8
• Add Covariance Functions by @gwaygenomics in #9
• Adding sparse random projection by @gwaygenomics in #10
• Adding Whitening Transform Method by @gwaygenomics in #13
• Adding feature_select.py function by @gwaygenomics in #15
• Adding Feature Select Testing by @gwaygenomics in #17
• Updating aggregate to work with sqlite files by @gwaygenomics in #16
• Adding random state set function in aggregate.py by @gwaygenomics in #18
• Add sqlalchemy to setup.py by @gwaygenomics in #19
• Adding codecov to travis by @gwaygenomics in #20
• Adding annotate.py by @gwaygenomics in #21
• Updating normalize.py by @gwaygenomics in #23
• Updating feature_select.py by @gwaygenomics in #24
• Inferring Features in feature_select.py by @gwaygenomics in #27
• Add Audit by @gwaygenomics in #33
• Try to coerce string input for subsample_n by @gwaygenomics in #34
• [hotfix] save quantile in audit by @gwaygenomics in #35
• [hotfix] make sure to enable audit output! by @gwaygenomics in #36
• Adding option to compress output data by @gwaygenomics in #40
• Blacklist features by @gwaygenomics in #41
• Inferring Cell Painting Features by @gwaygenomics in #42
• Add whitening by @gwaygenomics in #43
• Refactor Before PooledCellPainting by @gwaygenomics in #44
• Adding PooledCellPainting by @gwaygenomics in #45
• Add Init File in Pooled by @gwaygenomics in #46
• [Pooled] try to convert columns to numeric by @gwaygenomics in #47
• Adding MODZ Consensus Signature Operation by @gwaygenomics in #53
• Fixing MODZ to behave properly when not all metadata columns are specified by @gwaygenomics in #55
• Add write_gct function by @gwaygenomics in #56
• Upgrading Audit Functionality by @gwaygenomics in #60
• Functionality to Drop Outlier Features by @gwaygenomics in #62
• Fix aggregate dtype bug by @gwaygenomics in #65
• Remove kwargs everywhere by @gwaygenomics in #66
• Allowing feature and metadata feature setting in write_gct by @gwaygenomics in #67
• Add Feature Metadata to writing gct file by @gwaygenomics in #68
• Adding Robust Normalization by MAD by @gwaygenomics in #72
• Fix mad_robustize policy on low variance columns by @gwaygenomics in #74
• Enable cell counting with more than 2 defined strata by @gwaygenomics in #76
• Add CMAP options to annotate by @gwaygenomics in #73
• Abstract loading profiles and platemap by @gwaygenomics in #84
• Adding CSV sniffing for delimiters by @gwaygenomics in #85
• Fix missing value in variance threshold error by @gwaygenomics in #86
• Fix write_gct too much strip by @gwaygenomics in #87
• Switch to "samples='all'" as default and move operations to subfolder by @gwaygenomics in #88
• Updating whitening implementations by @gwaygenomics in #91
• clean pycytominer folder base to include core functionality by @gwaygenomics in #92
• changed whiten_method default by @AdeboyeML in #97
• Fix gzip sniffer by @gwaygenomics in #98
• Refactor the consensus.py file to keep consistent API by @gwaygenomics in #101
• Change whiten nomenclature to spherize by @gwaygenomics in #102
• increase modularity of infer_cp_features by @hillsbury in #103
• Setting up auto documentation with sphinx by @gwaygenomics in #104
• Updating theme and fixing RTD integration by @gwaygenomics in #105
• Adding pytest to requirements by @gwaygenomics in #106
• documentation edits by @bethac07 in #108
• Adding single cell module by @gwaygenomics in #111
• Updating consensus.py to also work with input files by @gwaygenomics in #115
• Output compression to ignore timestamps by @gwaygenomics in #119
• Subsampling at the point of single cell merging by @gwaygenomics in #121
• Refactoring annotate by @gwaygenomics in #118
• Fixing sphinx docs by @gwaygenomics in #124
• [hotfix] rename requirements doc by @gwaygenomics in #125
• Adding epsilon parameter to spherize by @gwaygenomics in #132
• Fix aggregate dropping samples by @gwaygenomics in #134
• Modify aggregate by @niranjchandrasekaran in #129
• Adding open source guideline documents by @gwaygenomics in #136
• Update README with Cell Painting paper URL by @shntnu in #139
• Set default object_feature to Metadata_ObjectNumber by @niranjchandrasekaran in #143
• Adding pipeline figure and boosting README by @gwaygenomics in #145
• Adding functionality to aggregate and annotate DeepProfiler output by @gwaygenomics in #78
• Replace travis with github actions by @niranjchandrasekaran in #151
• Replace aggregate_args by @niranjchandrasekaran in #148
• Update DeepProfiler Processing by @michaelbornholdt in #149
• add citation note by @gwaygenomics in #157
• cells.aggregate_compartment() queries the database in chunks, reducing memory by @sjfleming in #156
• Add "noise removal" feature selection by @ruifanp in #153
• fix issue when some samples have replicates and some don't by @bethac07 in #166
• Image features by @niranjchandrasekaran in #168
• Add Metadata_ prefix to count features in the image table by @niranjchandrasekaran in #171
• update pipeline by @michaelbornholdt in #163
• Remove step where image feature groups are capitalized by @niranjchandrasekaran in #173
• Citation.cff by @gwaygenomics in #182
• Fix dataframe reference in SingleCells function by @gwaygenomics in #183
• Add explicit documentation for variance_threshold freq_cut and unique_cut by @gwaygenomics in #184
• Update doc style by @gwaygenomics in #185
• Add github action to publish to pypi by @staylorx in #188

New Contributors

• @gwaygenomics made their first contribution in #1
• @AdeboyeML made their first contribution in #97
• @hillsbury made their first contribution in #103
• @bethac07 made their first contribution in #108
• @niranjchandrasekaran made their first contribution in #129
• @shntnu made their first contribution in #139
• @michaelbornholdt made their first contribution in #149
• @sjfleming made their first contribution in #156
• @ruifanp made their first contribution in #153
• @staylorx made their first contribution in #188

Full Changelog: https://github.com/cytomining/pycytominer/commits/v0.1